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2.2 Angstrom Resolution Crystal Structure of Nuclease Domain of Ribonuclase III (rnc) from Campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A11 PDB ENTRY 2A11
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein solution: 7.6 mg/mL, 0.5M Sodium chloride, 0.01M Tris pH 8.3
Screen solution: Classics II (F7), 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.4 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.099 α = 90 b = 98.252 β = 90 c = 118.41 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Si{1,1,1} 2010-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97965 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 30 99.9 0.118 16.7 7.3 18659 18659 -3 30.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.24 99.1 0.513 3.3 6.8 929
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2A11 2.205 29.6 17681 17681 952 99.91 0.17922 0.17922 0.17641 0.1824 0.23371 0.2462 RANDOM 26.785
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.97 2.81 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.363 r_dihedral_angle_3_deg 12.026 r_dihedral_angle_4_deg 9.328 r_scangle_it 5.311 r_scbond_it 3.276 r_dihedral_angle_1_deg 2.52 r_mcangle_it 2.163 r_angle_refined_deg 1.295 r_mcbond_it 1.187 r_angle_other_deg 0.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.363 r_dihedral_angle_3_deg 12.026 r_dihedral_angle_4_deg 9.328 r_scangle_it 5.311 r_scbond_it 3.276 r_dihedral_angle_1_deg 2.52 r_mcangle_it 2.163 r_angle_refined_deg 1.295 r_mcbond_it 1.187 r_angle_other_deg 0.847 r_mcbond_other 0.298 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2301 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling